normalize_total
Best62.9×
Median5.04×
Datasets6
pbmc68k · 32 threads322 ms to 4 ms
Single-cell genomics
scRNA-seq, deconvolution, trajectory, cell-cell communication
28
Tasks
16.7 ×
Median speedup
1482.3 ×
Peak speedup
Accelerated tasks
28 of 28 tasks shown
Preprocessing
8 tasksNormalizeData
Best43.7×
Median10.7×
Datasets6
pbmc200k_glaucoma · 32 threads15.00 s to 340 ms
ScaleData
Best24.7×
Median7.36×
Datasets7
pbmc68k · 32 threads2.51 s to 110 ms
highly_variable_genes
Best19.6×
Median4.59×
Datasets6
pbmc68k · 4 threads283 ms to 15 ms
SCTransform
Best16.7×
Median8.71×
Datasets6
pbmc200k_glaucoma · 32 threads20.85 min to 1.25 min
FindVariableFeatures
Best14.2×
Median8.33×
Datasets7
gastrulation_pijuansala · 4 threads19.98 s to 1.41 s
scale
Best9.50×
Median5.70×
Datasets6
pbmc68k · 4 threads540 ms to 57 ms
highly_variable_genes (v3 · batched)
Best9.31×
Median6.06×
Datasets5
pbmc200k_glaucoma · 32 threads5.05 s to 543 ms
Dimensionality reduction
2 tasksGraph + clustering
2 tasksFindNeighbors
Best4.23×
Median2.38×
Datasets7
tms_ss2 · 32 threads20.10 s to 5.59 s
leiden
Best1.77×
Median1.60×
Datasets6
tms_ss2 · 1 threads3.35 s to 1.89 s
Differential expression
2 tasksrank_genes_groups
Best293.3×
Median26.4×
Datasets6
pbmc68k · 14 threads19.63 s to 66 ms
FindAllMarkers
Best271.4×
Median123.4×
Datasets7
tms_ss2 · 32 threads24.90 min to 5.50 s
Integration
1 taskIntegrateLayers · CCA
Best30.1×
Median9.41×
Datasets6
tms_ss2_cca_111k · 1 threads146.18 min to 4.86 min
Cell-cell communication
4 tasksNicheNet
Best1,482×
Median676.5×
Datasets5
lcmv_mouse_full · 8 threads2.08 min to 94 ms
computeCommunProb
Best711.2×
Median63.2×
Datasets5
ifnb_2k · 4 threads1.59 min to 136 ms
call
Best81.8×
Median20.8×
Datasets5
cpdb_heart_t22_c2200 · 1 threads22.63 min to 16.59 s
GenerateCCIM
Best3.01×
Median2.67×
Datasets5
heart_adult_ccim_1k4 · 1 threads2.70 min to 53.96 s
CNV inference
1 taskinferCNV (HMM)
inferCNV (HMM)
Best76.6×
Median43.6×
Datasets5
gbm_neftel_large · 1 threads6.74 min to 5.28 s
Compositional analysis
1 taskscCODA
Best1.76×
Median1.46×
Datasets5
ifnb_pseudo · 1 threads34.23 s to 19.43 s
Differential expression & markers
2 taskstradeSeq · fitGAM
Best7.04×
Median3.00×
Datasets5
fitgam_ood_2lin_3000g_3500c · 8 threads3.48 min to 29.67 s
MAST
Best6.38×
Median3.33×
Datasets5
pbmc68k_50k · 8 threads1.56 min to 14.39 s
Quality control
1 taskdecontX
Best3.67×
Median1.35×
Datasets5
ext_hgmm_chemistry_20k_3p_HT · 8 threads4.99 min to 1.38 min
Spatial & deconvolution
2 tasksrun.RCTD
Best23.7×
Median11.6×
Datasets5
lymph_node_rctd_10000_boot · 1 threads38.95 min to 1.72 min
cell2location.models.Cell2location.train
Best2.82×
Median2.23×
Datasets5
lymph_node_3000_seed42_10lineage · 4 threads4.42 min to 1.57 min
Trajectory & dynamics
2 tasksscvelo.tl.recover_dynamics
Best10.7×
Median2.70×
Datasets5
pancreas · 1 threads5.47 min to 30.69 s
slingshot
Best8.96×
Median3.60×
Datasets5
pbmc68k_tiny · 1 threads59.82 s to 6.67 s